Re: [AMBER-Developers] Oddities in runmd.F90 in pmemd

From: Scott Le Grand <>
Date: Thu, 13 Dec 2012 14:27:50 -0800

As noted in the bug report:

1) Pressure scaling is all done in one place for the GPU:

    if (gpu->sim.constraints > 0)

Whatever's going on (and I suspect it's ultimately FPRE) it's not that or
it would blow up a lot sooner...

2) While the else looks strange, it appears to be the end case for chain
starting at line 1214 if (ntp .eq. 1) with an else if (ntp .eq 2) at line
1221 finished by the else at line 1257 (not my code though)...

On Thu, Dec 13, 2012 at 11:40 AM, Duke, Robert E Jr <>wrote:

> Hmmm, all past my tenure on pmemd itself, as I expect you know. I am
> buried in the amoeba code for right now, but will be interested in going
> back to see what happened to pmemd in the time period I have not been
> working on it when I get time. I would think the origin of npt could be
> tracked down, and I would agree it is not the correct way to fix a typo...
> It did not exist in Amber 10. Scott?
> - Bob
> ________________________________________
> From: David A Case []
> Sent: Thursday, December 13, 2012 5:54 AM
> To:
> Subject: [AMBER-Developers] Oddities in runmd.F90 in pmemd
> (1) about the problem that occurs when ntr=1, ntp=1 on GPU:
> In the CPU code, when ntp>0 and ntr=1, there is a call to
> pressure_scale_restraint_crds(). But there is no gpu equivalent to
> this.
> Assuming that the restraint coordinates acutally used are the ones on
> the
> gpu(?), this looks like an error.
> (2) There are several places where a specific if has been commented out,
> and replaced with a generic else: e.g. at about line 1257:
> !else if (npt .gt. 2) then
> else
> Is there a reason for this? the effect of the above changes is that
> the following section is run even when ntp = 0, which looks wrong. Is
> it
> just that "npt" above is a typo (should be "ntp"), and was fixed in a
> funny way? Similar thing happens (but with no typo) for the csurften==3
> option.
> ...thx...dac
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Received on Thu Dec 13 2012 - 14:30:01 PST
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